Mechanical role of a protein droplet in endocytosis

Acknowledgements

Lab meeting goals

• make the model understandable to everyone
• get feedback on whether the model constraints make biological sense

Background/motivation

Src homology 3 (SH3) domains and proline-rich motifs (PRMs) are enriched in CME

• ~40-fold enrichment of SH3 domains in CME proteins
• 29 out of ~60 CME proteins participate in SH3-PRM interactome
• Multiple SH3 or PRM per protein

[tonikian_bayesian_2009]

Multivalent SH3-PRM proteins undergo liquid-liquid phase separation (LLPS)

[li_phase_2012]

Hypothesis: CME proteins can undergo LLPS

Hypothetical roles of LLPS in CME

Evidence for LLPS-mediated membrane bending

[yuan_membrane_2020]

[bergeron-sandoval_endocytosis_2017]

Model walk-through

Full model

\(F=\sigma\left(S_{0}+S_{m}+S_{i}\right)+\frac{K}{2} S_{i}\left(\frac{2}{R_{i}}-C_{i}\right)^{2}+\gamma_{d} S_{d}-\gamma_{m} S_{m}-\gamma_{i} S_{i}+P V_{i}\)

Energy contributions from membrane alone

membrane tension

\(\sigma\left(S_{0}+S_{m}+S_{i}\right)\)

Energy contributions from membrane alone

bending energy

\(\frac{K}{2} S_{i}\left(\frac{2}{R_{i}}-C_{i}\right)^{2}\)

Energy contributions from membrane alone

combined membrane tension and bending energy

\(F=\sigma\left(S_{0}+S_{m}+S_{i}\right)+\frac{K}{2} S_{i}\left(\frac{2}{R_{i}}-C_{i}\right)^{2}\)

Energy contributions from droplet + membrane

surface tension

\(\gamma_{d} S_{d}\)

Energy contributions from droplet + membrane

wetting energy (note: negative contribution!)

\(\gamma_{m} S_{m}+\gamma_{i} S_{i}\)

Energy contributions from droplet + membrane

combined surface tension and wetting energy

\(F=\gamma_{d} S_{d}-\gamma_{m} S_{m}-\gamma_{i} S_{i}\)

Energy contributions from turgor pressure

\(P V_{i}\)

All contributions together

\(F=\sigma\left(S_{0}+S_{m}+S_{i}\right)+\frac{K}{2} S_{i}\left(\frac{2}{R_{i}}-C_{i}\right)^{2}+\gamma_{d} S_{d}-\gamma_{m} S_{m}-\gamma_{i} S_{i}+P V_{i}\)

Some preliminary parameter explorations

Changes in surface areas explain driving force

\(F=\sigma\left(S_{0}+S_{m}+S_{i}\right)+\frac{K}{2} S_{i}\left(\frac{2}{R_{i}}-C_{i}\right)^{2}+\gamma_{d} S_{d}-\gamma_{m} S_{m}-\gamma_{i} S_{i}+P V_{i}\)

Changes in surface area drive internalization through wetting energy and surface tension

Changes in surface area drive internalization through wetting energy and surface tension

Changes in surface area drive internalization through wetting energy and surface tension

Relative strength of wetting energy vs. surface tension sets driving force

Droplet cannot overcome very high turgor pressure

Future directions

• Devise solution for when droplet is smaller than invagination
• Implement more sophisticated membrane geometry model with continuous curvature
• Gain a deeper understanding of why the model works: build more intuitive plots to get a sense of which parameters are most sensitive
• Any inspiration for experimental design?

References

• [bergeron-sandoval_endocytosis_2017] Bergeron-Sandoval, Heris, Hendricks, Ehrlicher, Francois, Pappu & Michnick, Endocytosis Caused by Liquid-Liquid Phase Separation of Proteins, bioRxiv, 145664 (2017).
• [lacy_molecular_2018] Lacy, Ma, Ravindra & Berro, Molecular Mechanisms of Force Production in Clathrin-Mediated Endocytosis, FEBS Letters, 592(21), 3586-3605 (2018).
• [li_phase_2012] Li, Banjade, Cheng, Kim, Chen, Guo, Llaguno, Hollingsworth, King, Banani, Russo, Jiang, Nixon & Rosen, Phase Transitions in the Assembly of Multivalent Signalling Proteins, Nature, 483(7389), 336-340 (2012).
• [tonikian_bayesian_2009] Tonikian, Xin, Toret, Gfeller, Landgraf, Panni, Paoluzi, Castagnoli, Currell, Seshagiri, Yu, Winsor, Vidal, Gerstein, Bader, Volkmer, Cesareni, Drubin, Kim, Sidhu & Boone, Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins, PLoS Biology, 7(10), (2009).
• [yuan_membrane_2020] Yuan, Alimohamadi, Bakka, Trementozzi, Fawzi, Rangamani & Stachowiak, Membrane Bending by Protein Phase Separation, bioRxiv, 2020.05.21.109751 (2020).